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Puzzle 542
Puzzle 542 Advanced Alignment Cutpoint Puzzle Same protein as Puzzle 369 CASP9 Puzzle 38 PDB id 2L3B Solution NMR structure of BT_0084, a conjugative transposon lipoprotein from Bacteroides thetaiotamicron. Ramelot, T.A., Yang, Y., Xiao, R., Acton, T.B., Everett, J.K., Montelione, G.T., Kennedy, M.A., Irc 198325 1334878304 E1 AD gmn.png Irc 198325 1334878266 E1 AD gmn.png Irc 82314 1334878498 S3 Boots.png Irc 82314 1334878364 S3 Boots.png Irc 82314 1334876953 S3 Boots.png Irc 82314 1334876930 S3 Boots.png Irc 82314 1334876917 S3 BootsMcgraw.png Irc 82314 1334878389 S3 Boots.png Irc 198325 1334878372 S4 gmn.png Irc 198325 1334878390 S4 gmn.png Irc 215720 1334876733 S6 PaulDunn.png Irc 215720 1334876755 S6 PaulDunn.png irc_179219_1334882456 S2 spmm.png irc_163073_1334881878 S1 RabidNimravid.png irc_163073_1334881895 S1 RabidNimravid.png 01:34:16 @boots--did you use threaded temp? 01:38:36 @boots--yeah, i got lucky with a quick evo from RabidNimravid :P 01:39:21 @gmn: I was just happy that I was able to untwist that beast into something almost good-looking. 01:39:31 lol 01:39:42 i did it as de novo :P 01:39:53 Seriously... When I did the alignment, the score was negative infinity. 01:40:08 AFter a shake and a wiggle, it was still -750K. 01:40:08 same here 01:40:22 I thought my -246000 was bad. 01:40:27 wow 01:40:29 I did a lot of manual work to het the score over zero. 01:41:15 i just took straight chain and aligned sheets--never liked the threaded temp 01:41:31 With six cutpoints? I don't blame you. 01:41:40 lol 01:41:56 <@MikeCassidyToo> Today mine was -1007942.737 pts 01:42:20 No that was your gain 01:42:38 <@MikeCassidyToo> after getting it to 8900 or something i quit 01:43:15 <@MikeCassidyToo> I never really had an idea what to do with it 01:43:15 It took me about 2 hours to clean up after alignment 01:43:44 this was a tough one for sure to get usuable structures 01:45:05 i folded 542 from the unwrapped start too. but mostly because i found the alignment confusing, since it's the first time i've needed to use it. somehow got 23rd with it 01:45:33 nice, ghost-white 01:53:16 542 was an exercize for cutpoints. To clean up after closing I did select the bad parts and wiggle lllloooonnng 01:53:33 Has anybody found a better way? 01:53:48 @timo--not me 01:54:13 @Timo: You need to manually rebuild the short section on either side of the cutpoint, maybe 5 residues in total. 01:54:14 sounds like boots has a method though 01:54:30 Then locla wiggle the section. 01:54:36 ....local wiggle... 01:54:51 Boots, that did not work for me, tried that a few times 01:55:14] @Timo; I had to do it several times to make it work. 01:55:32 The rebuild did nothing for the backbone score 01:55:42 What do you do before closing the cutpoints? 01:55:43 nor for me, timo--i must be too impatient :P 01:55:50 only wiggle worked 01:56:00 but slow 01:56:01 I swear, I made mine jump from negative hundred of thousands to negatove thousands. 01:56:32 And then, using GAB, it brought the score into the positives. 01:56:35 But those neg thousands took forever 01:57:32 @Datacute: I manually moved the cut pieces closer together before I joined them. 01:57:58 Not by cut and paste, but by rebuilding/stretching them. 01:58:08 i got my threaded version to about 10200--never higher--after a lot of manual and script work :P 01:58:56 @Boots, I also selected a few either side, and local wiggled before removing the cut pot. I don't know if that makes any difference to the resulting cut removed segment 01:59:35 @ Data: I am not sure, since cutpoints are a very new type of puzzle, and I don't have much experience with them. 01:59:45 bbl--and again--nice work folders on 542 01:59:52 data was that fast? 02:00:00 his stetson to gmn 02:00:37 Timo, yes 02:01:08 Not too dirty negatives then? 02:02:06 Still got them, but wiggling before removing them seemed to work better - especially when one of the parts wiggling wasn't constrained by being joined to other non-wiggign segments - i.e. at an end Category:Puzzle Results Category:Beta